therMizer

The remotes package is needed to install packages hosted on GitHub.

remotes::install_github("sizespectrum/therMizer@dev")

Downloading GitHub repo sizespectrum/therMizer@dev

These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                  
 2: CRAN packages only                   
 3: None                                 
 4: colorspace  (2.0-3  -> 2.1-0 ) [CRAN]
 5: cli         (3.6.0  -> 3.6.1 ) [CRAN]
 6: rlang       (1.0.6  -> 1.1.0 ) [CRAN]
 7: vctrs       (0.5.2  -> 0.6.1 ) [CRAN]
 8: utf8        (1.2.2  -> 1.2.3 ) [CRAN]
 9: pillar      (1.8.1  -> 1.9.0 ) [CRAN]
10: fansi       (1.0.3  -> 1.0.4 ) [CRAN]
11: fastmap     (1.1.0  -> 1.1.1 ) [CRAN]
12: digest      (0.6.29 -> 0.6.31) [CRAN]
13: htmltools   (0.5.4  -> 0.5.5 ) [CRAN]
14: Rcpp        (1.0.9  -> 1.0.10) [CRAN]
15: hms         (1.1.2  -> 1.1.3 ) [CRAN]
16: xfun        (0.36   -> 0.37  ) [CRAN]
17: curl        (4.3.2  -> 5.0.0 ) [CRAN]
18: gtable      (0.3.1  -> 0.3.3 ) [CRAN]
19: tibble      (3.1.7  -> 3.2.1 ) [CRAN]
20: dplyr       (1.1.0  -> 1.1.1 ) [CRAN]
21: htmlwidgets (1.6.1  -> 1.6.2 ) [CRAN]

1

colorspace  (2.0-3  -> 2.1-0 ) [CRAN]
cli         (3.6.0  -> 3.6.1 ) [CRAN]
rlang       (1.0.6  -> 1.1.0 ) [CRAN]
vctrs       (0.5.2  -> 0.6.1 ) [CRAN]
utf8        (1.2.2  -> 1.2.3 ) [CRAN]
pillar      (1.8.1  -> 1.9.0 ) [CRAN]
fansi       (1.0.3  -> 1.0.4 ) [CRAN]
fastmap     (1.1.0  -> 1.1.1 ) [CRAN]
digest      (0.6.29 -> 0.6.31) [CRAN]
htmltools   (0.5.4  -> 0.5.5 ) [CRAN]
Rcpp        (1.0.9  -> 1.0.10) [CRAN]
hms         (1.1.2  -> 1.1.3 ) [CRAN]
xfun        (0.36   -> 0.37  ) [CRAN]
curl        (4.3.2  -> 5.0.0 ) [CRAN]
gtable      (0.3.1  -> 0.3.3 ) [CRAN]
tibble      (3.1.7  -> 3.2.1 ) [CRAN]
dplyr       (1.1.0  -> 1.1.1 ) [CRAN]
htmlwidgets (1.6.1  -> 1.6.2 ) [CRAN]

Installing 18 packages: colorspace, cli, rlang, vctrs, utf8, pillar, fansi, fastmap, digest, htmltools, Rcpp, hms, xfun, curl, gtable, tibble, dplyr, htmlwidgets
Installing packages into ‘C:/Users/kjmurphy/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)

  There are binary versions available but the source versions are later:

  Binaries will be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/colorspace_2.1-0.zip'
Content type 'application/zip' length 2628973 bytes (2.5 MB)
downloaded 2.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/cli_3.6.0.zip'
Content type 'application/zip' length 1297129 bytes (1.2 MB)
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/rlang_1.1.0.zip'
Content type 'application/zip' length 1571771 bytes (1.5 MB)
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/vctrs_0.6.1.zip'
Content type 'application/zip' length 1337511 bytes (1.3 MB)
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/utf8_1.2.3.zip'
Content type 'application/zip' length 149929 bytes (146 KB)
downloaded 146 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/pillar_1.9.0.zip'
Content type 'application/zip' length 658759 bytes (643 KB)
downloaded 643 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/fansi_1.0.4.zip'
Content type 'application/zip' length 311830 bytes (304 KB)
downloaded 304 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/fastmap_1.1.1.zip'
Content type 'application/zip' length 129698 bytes (126 KB)
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/digest_0.6.31.zip'
Content type 'application/zip' length 195097 bytes (190 KB)
downloaded 190 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/htmltools_0.5.4.zip'
Content type 'application/zip' length 350881 bytes (342 KB)
downloaded 342 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/Rcpp_1.0.10.zip'
Content type 'application/zip' length 2813037 bytes (2.7 MB)
downloaded 2.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/hms_1.1.3.zip'
Content type 'application/zip' length 103015 bytes (100 KB)
downloaded 100 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/xfun_0.37.zip'
Content type 'application/zip' length 413121 bytes (403 KB)
downloaded 403 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/curl_5.0.0.zip'
Content type 'application/zip' length 2621374 bytes (2.5 MB)
downloaded 2.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/gtable_0.3.3.zip'
Content type 'application/zip' length 225822 bytes (220 KB)
downloaded 220 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/tibble_3.2.1.zip'
Content type 'application/zip' length 690255 bytes (674 KB)
downloaded 674 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/dplyr_1.1.1.zip'
Content type 'application/zip' length 1553410 bytes (1.5 MB)
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/htmlwidgets_1.6.2.zip'
Content type 'application/zip' length 810835 bytes (791 KB)
downloaded 791 KB

package ‘colorspace’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘colorspace’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\colorspace\libs\x64\colorspace.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\colorspace\libs\x64\colorspace.dll: Permission deniedWarning: restored ‘colorspace’

package ‘cli’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘cli’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\cli\libs\x64\cli.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\cli\libs\x64\cli.dll: Permission deniedWarning: restored ‘cli’

package ‘rlang’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘rlang’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\rlang\libs\x64\rlang.dll: Permission deniedWarning: restored ‘rlang’

package ‘vctrs’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘vctrs’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\vctrs\libs\x64\vctrs.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\vctrs\libs\x64\vctrs.dll: Permission deniedWarning: restored ‘vctrs’

package ‘utf8’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘utf8’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\utf8\libs\x64\utf8.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\utf8\libs\x64\utf8.dll: Permission deniedWarning: restored ‘utf8’

package ‘pillar’ successfully unpacked and MD5 sums checked
package ‘fansi’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘fansi’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\fansi\libs\x64\fansi.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\fansi\libs\x64\fansi.dll: Permission deniedWarning: restored ‘fansi’

package ‘fastmap’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘fastmap’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\fastmap\libs\x64\fastmap.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\fastmap\libs\x64\fastmap.dll: Permission deniedWarning: restored ‘fastmap’

package ‘digest’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘digest’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\digest\libs\x64\digest.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\digest\libs\x64\digest.dll: Permission deniedWarning: restored ‘digest’

package ‘htmltools’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘htmltools’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\htmltools\libs\x64\htmltools.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\htmltools\libs\x64\htmltools.dll: Permission deniedWarning: restored ‘htmltools’

package ‘Rcpp’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘Rcpp’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\Rcpp\libs\x64\Rcpp.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\Rcpp\libs\x64\Rcpp.dll: Permission deniedWarning: restored ‘Rcpp’

package ‘hms’ successfully unpacked and MD5 sums checked
package ‘xfun’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘xfun’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\xfun\libs\x64\xfun.dll: Permission deniedWarning: restored ‘xfun’

package ‘curl’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘curl’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\curl\libs\x64\curl.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\curl\libs\x64\curl.dll: Permission deniedWarning: restored ‘curl’

package ‘gtable’ successfully unpacked and MD5 sums checked
package ‘tibble’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘tibble’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\tibble\libs\x64\tibble.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\tibble\libs\x64\tibble.dll: Permission deniedWarning: restored ‘tibble’

package ‘dplyr’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘dplyr’Warning: problem copying C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\00LOCK\dplyr\libs\x64\dplyr.dll to C:\Users\kjmurphy\AppData\Local\R\win-library\4.2\dplyr\libs\x64\dplyr.dll: Permission deniedWarning: restored ‘dplyr’

package ‘htmlwidgets’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\kjmurphy\AppData\Local\Temp\RtmpQX4k8m\downloaded_packages

Running `R CMD build`...

* checking for file 'C:\Users\kjmurphy\AppData\Local\Temp\RtmpQX4k8m\remotes30986b98b54\sizespectrum-therMizer-0521192/DESCRIPTION' ... OK
* preparing 'therMizer':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted 'LazyData' from DESCRIPTION
* building 'therMizer_0.1.0.tar.gz'

Installing package into ‘C:/Users/kjmurphy/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)

* installing *source* package 'therMizer' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'mizer' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace 'rlang' 1.0.6 is already loaded, but >= 1.1.0 is required
Execution halted
ERROR: lazy loading failed for package 'therMizer'
* removing 'C:/Users/kjmurphy/AppData/Local/R/win-library/4.2/therMizer'
* restoring previous 'C:/Users/kjmurphy/AppData/Local/R/win-library/4.2/therMizer'

Warning: installation of package ‘C:/Users/kjmurphy/AppData/Local/Temp/RtmpQX4k8m/file30981648f95/therMizer_0.1.0.tar.gz’ had non-zero exit status

Load the newly installed package with

library(therMizer)

Error in library(therMizer) : there is no package called ‘therMizer’

Adding min and max temp for each group

Using sealifebase for all non-fish species/groups. In most cases, there are no listed Temperature values in the ‘Environment’ section, like there is for more data-rich species, e.g., cod

Instead, there are values at the bottom of the sealifebase pages in ‘Estimates of some properties based on models’ with ‘Preferred temperature’ estimates from the AquaMaps model-based approach (https://www.gbif.org/tool/81356/aquamaps-predicted-range-maps-for-aquatic-species)

[1] “euphausiids”: Antarctic krill - (Preferred temperature (Ref. 115969): -1.5 - 1.6, mean 0.2 (based on 535 cells)) Crystal krill - (Preferred temperature (Ref. 115969): -1.8 - 1.1, mean -1.6 (based on 3588 cells)) Thysanoessa macrura - (Preferred temperature (Ref. 115969): -1.2 - 2.8, mean 0.2 (based on 24 cells). Not included due to small number of cells and low contribution to biomass in this model domain [2]“mesopelagic fishes” - Electrona antarctica(nothing on fishbase)
[3]“bathypelagic fishes”
[4]“shelf and coastal fishes”: Marbled rockcod (-1 - 5) [5]“flying birds”: Southern giant petrel (Preferred temperature (Ref. 115969): 2.1 - 15.6, mean 10.1 (based on 533 cells)); Arctic tern (Sterna paradisaea) (Preferred temperature (Ref. 115969): 0.4 - 13.3, mean 6.8 (based on 2468 cells)) Thalassarche chrysostoma (Grey-headed petrel) (Preferred temperature (Ref. 115969): 1.3 - 9.1, mean 5.2 (based on 263 cells)) South polar skua (Preferred temperature (Ref. 115969): 0.2 - 18.2, mean 6.4 (based on 1318 cells)) Diomedea exulans (Wandering albatross), (Preferred temperature (Ref. 115969): 0.5 - 12, mean 4.6 (based on 1528 cells)_ [6]“small divers” - no info for adelie, gentoo or crested penguins on sealifebase. Guess based on medium divers
[7]“squids” - based on Psychroteuthis glacialis (sealifebase)
[8]“toothfishes” - no data on fishbase
[9]“leopard seals” - Preferred temperature (Ref. 115969): -1.9 - 1.4, mean -0.5 (based on 2109 cells).
[10] “medium divers”: Crabeater Seals - (Preferred temperature (Ref. 115969): -0.4 - 1, mean 0.1 (based on 9397 cells)) Ross seals (Preferred temperature (Ref. 115969): -1.8 - 1.1, mean -1.5 (based on 2110 cells)); Weddell seals (Preferred temperature (Ref. 115969): -1.8 - 1, mean -1.6 (based on 6026 cells)); Hourglass dolphin (Preferred temperature (Ref. 115969): 0.1 - 2, mean 0.9 (based on 11222 cells)) # Not included in the biomass King penguin (no data on sealifebase) Emperor penguin (no data on sealifebase) [11]“large divers” - Southern elephant seals only in this group now that Sperm whales are also seperated
[12]“minke whales”
[13]“orca”
[14]“sperm whales”
[15]“baleen whales”

species_params(params)$temp_min <- c(-1.8, # euphausiids
                                     -2, # mesopelagic fishes
                                     -2, # bathypelagic fishes
                                     -1, # "shelf and coastal fishes" 
                                     0.2, # "flying birds"
                                     -0.4, # "small divers"             
                                     -0.8, # "squids"                  
                                     -2, # "toothfishes"              
                                     -1.9, # "leopard seals"           
                                     -0.4, # "medium divers"            
                                     0.1, # "large divers"             
                                     0.2, # "minke whales"             
                                     0.3, # "orca"                     
                                     0.3, # "sperm whales"             
                                     0.2) # "baleen whales"

species_params(params)$temp_max <- c(1.6, # euphausiids
                                     5, # mesopelagic fishes
                                     5, # bathypelagic fishes
                                     5, # "shelf and coastal fishes" 
                                     18.2, # "flying birds"
                                     1, # "small divers"             
                                     1.1, # "squids"                  
                                     5, # "toothfishes"              
                                     1.4, # "leopard seals"           
                                     1, # "medium divers"            
                                     1.6, # "large divers"             
                                     7, # "minke whales"             
                                     13.1, # "orca"                     
                                     3.8, # "sperm whales"             
                                     10.2) # "baleen whales"